Character Definition | A,C,G,U,* // Identity and order of characters in matrices
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [16] // Initial node
ClusterNode  | Deletion Probability [0.000000000000000000000000000001205039292532039249129520049423] | Num Left Bases [7] | Num Right Bases [4] | Left Index [1] | Right Index [16] | Norm Constant [0.043112858039458] // Cluster node 8HZL|1|B|G|5:8HZL|1|B|A|13 and 8HZL|1|B|A|77:8HZL|1|B|C|80
Interaction  | Interacting Bases [3,8] | Pair Probability [[0.018414538,0.004075167,0.019126511,0.004075167,0.000000000],[0.040981170,0.328380556,0.004075167,0.004075167,0.000000000],[0.004075167,0.009768444,0.030991298,0.018124938,0.000000000],[0.445978203,0.004075167,0.023643628,0.040139714,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8HZL|1|B|U|8 - 8HZL|1|B|A|77 tWH 
Interaction  | Interacting Bases [2,10] | Pair Probability [[0.719495317,0.052527140,0.006810338,0.032555776,0.000000000],[0.010233124,0.004965314,0.004056495,0.004968922,0.000000000],[0.001362068,0.004062330,0.125954217,0.007676480,0.000000000],[0.006503390,0.004967710,0.007510355,0.006351024,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8HZL|1|B|A|6 - 8HZL|1|B|A|79 tWW 
Interaction  | Interacting Bases [1,11] | Pair Probability [[0.009546506,0.019881954,0.010870922,0.197449200,0.000000000],[0.016768697,0.009361308,0.199122279,0.013028540,0.000000000],[0.010750195,0.243371713,0.002049102,0.026250458,0.000000000],[0.194922229,0.013522366,0.023009709,0.010094826,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8HZL|1|B|G|5 - 8HZL|1|B|C|80 cWW 
Interaction  | Interacting Bases [1,6] | Pair Probability [[0.161781521,0.161006430,0.002010824,0.009723179,0.000000000],[0.188168590,0.008866353,0.002010824,0.008039245,0.000000000],[0.239543895,0.002010824,0.002010824,0.006594167,0.000000000],[0.174016311,0.008738957,0.015821944,0.009656115,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8HZL|1|B|G|5 - 8HZL|1|B|A|12 tSW 
Interaction  | Interacting Bases [2,7] | Pair Probability [[0.699352762,0.056568352,0.006608912,0.029863825,0.000000000],[0.001321782,0.005609178,0.003274235,0.001321782,0.000000000],[0.116604962,0.001321782,0.048585315,0.006335302,0.000000000],[0.001321782,0.001321782,0.014147945,0.006440300,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8HZL|1|B|A|6 - 8HZL|1|B|A|13 tHW 
Interaction  | Interacting Bases [8,9] | Pair Probability [[0.101162013,0.149864007,0.005458946,0.042594928,0.000000000],[0.097642401,0.096422023,0.001114025,0.009048953,0.000000000],[0.009715720,0.001114025,0.101175273,0.091507080,0.000000000],[0.101531566,0.100311520,0.001114025,0.090223496,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8HZL|1|B|A|77 - 8HZL|1|B|C|78 cSH 
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.016666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.016666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.950000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.016666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 8HZL|1|B|G|9
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.750000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 8HZL|1|B|A|11
Insertion    | Location [2] | Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Letter Distribution [0.083333333,0.083333333,0.083333333,0.750000000,0.000000000]// Insertion after nucleotide 2, position 2 in cluster node
Insertion    | Location [4] | Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Letter Distribution [0.083333333,0.083333333,0.083333333,0.750000000,0.000000000]// Insertion after nucleotide 4, position 4 in cluster node
InitialNode  | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [8] | Right Index [12] // Initial node 8HZL|1|B|C|14 - 8HZL|1|B|G|76 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.750000000,0.083333333,0.083333333,0.000000000] | Position [1] | Left Index [8] | Right Index [12] // Fixed node on left for 8HZL|1|B|A|12
InitialNode  | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [12] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.110577593,0.111399105,0.171202567,0.123434124,0.000000000],[0.117061285,0.116790218,0.001327410,0.116159705,0.000000000],[0.001327410,0.001327410,0.006489287,0.001327410,0.000000000],[0.006256089,0.001327410,0.112665566,0.001327410,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [12] // Basepair A15 - G76 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009203552,0.018544658,0.010295215,0.194997478,0.000000000],[0.019194364,0.009501956,0.196157927,0.011930519,0.000000000],[0.010244330,0.217046390,0.002027020,0.024427390,0.000000000],[0.216938755,0.011848709,0.037639682,0.010002057,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [10] | Right Index [11] // Basepair G16 - C75 cWW 
HairpinNode  | Num Bases [1] | Left Index [11] | Right Index [11] | Norm Constant [1.000000000000000] // Hairpin node type *
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,1.000000000]] // Hairpin for truncation
